cc-qtl-db issueshttps://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues2023-10-26T15:28:25+02:00https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/83Help input file experiments2023-10-26T15:28:25+02:00Remi PLANELHelp input file experiments0.2.0-stableRemi PLANELRemi PLANELhttps://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/127Try to not use encoded id for galaxy interactions2023-10-26T15:26:15+02:00Remi PLANELTry to not use encoded id for galaxy interactionsThe encoded ids in Galaxy can change if the seed do.
Try to figure out how to identify: histories, workflow and invocation using only names.
It should be possible and then from that get the encoded ids to interacte with bioblend api.
Th...The encoded ids in Galaxy can change if the seed do.
Try to figure out how to identify: histories, workflow and invocation using only names.
It should be possible and then from that get the encoded ids to interacte with bioblend api.
This should solve the planemo problem with docker.https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/243Rename phenotypes / phenotype categories2023-10-04T13:03:21+02:00Remi PLANELRename phenotypes / phenotype categories- [ ] Phenotypes -> Traits and covars record in db
- [ ] Phenotypes categories -> Traits and covars group- [ ] Phenotypes -> Traits and covars record in db
- [ ] Phenotypes categories -> Traits and covars groupmeeting 04/10Remi PLANELRemi PLANELhttps://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/242permutations boundaries2023-10-04T13:03:21+02:00Remi PLANELpermutations boundaries- Set in Galaxy wrapper limit (100,20000)
- the same in web interface form- Set in Galaxy wrapper limit (100,20000)
- the same in web interface formmeeting 04/10Remi PLANELRemi PLANELhttps://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/130Update help menus in interface2023-07-19T14:55:45+02:00Victoire BAILLETUpdate help menus in interfaceInterface has multiple help menus which need to be updated for current version of ccqtl (covariates, multiple phenotypes, etc).
This issue = @vibaille reporting to @rplanel the help menus to be updated and the new text.
One reply == o...Interface has multiple help menus which need to be updated for current version of ccqtl (covariates, multiple phenotypes, etc).
This issue = @vibaille reporting to @rplanel the help menus to be updated and the new text.
One reply == one help menu (screenshot) and the next text to put in there.Remi PLANELRemi PLANELhttps://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/121Todo list for future milestone2023-05-11T11:45:52+02:00Victoire BAILLETTodo list for future milestoneThis is to-do list for future milestone (the one that will come next, after conda packaging of ongoing valpha)
- [ ] current work is based on R 4.2. Move to R new version (4.3 or any updated version at time of novel milestone). That may ...This is to-do list for future milestone (the one that will come next, after conda packaging of ongoing valpha)
- [ ] current work is based on R 4.2. Move to R new version (4.3 or any updated version at time of novel milestone). That may require rewriting a bit the code, see https://cran.r-project.org/doc/manuals/r-release/NEWS.html
- [ ] move to r/qtl2 novel release (version 0.32), current work is based on qtl2 0.30.
- [ ] incorporate m39 (moving to qtl2 v 0.32 may turn helpful for parsing the sqlite, but overall this whole part needs to be rewritten in accordance with the display in interface to make it robust to both m38 and m39)
- [ ] add FDR as option for multiple testing, see issue #120
- [ ] in code then interface, make recap table Peak start stop markers etc, see issue #89
- [ ] Fix pmap/gmap use all across the code
- [ ] Fix filenames formatting for the peaks, refined regions, etc - no need to display in bp, poorly readable, think abt something new
- [ ] In refine regions, indexing to prune equivalent snps prior to top snps and/or assohttps://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/7Behavioural data examples - Protocol description2023-05-05T11:52:06+02:00Elodie EYBehavioural data examples - Protocol description**Example of information that should be available to describe the protocol:**
Name of protocol (example: Protocol A)
social or single
duration of the test (long-term or short-term experiment, if we want it simple)
Text field where to...**Example of information that should be available to describe the protocol:**
Name of protocol (example: Protocol A)
social or single
duration of the test (long-term or short-term experiment, if we want it simple)
Text field where to describe briefly the protocol (not for query in the database but for the user)?https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/9Behavioural data examples - Data collected for one animal2023-05-05T11:51:58+02:00Elodie EYBehavioural data examples - Data collected for one animal**Examples of data collected for one animal in one experiment with protocol A:**
animalID
date of experiment (with the date of the experiment, the age of the animal at testing can be found back easily, without any problem of conversion...**Examples of data collected for one animal in one experiment with protocol A:**
animalID
date of experiment (with the date of the experiment, the age of the animal at testing can be found back easily, without any problem of conversion in days of months or weeks if we enter directly the age)
Protocol used: Protocol A
Var1, Var2, Var3... VarX
These variables are continuous; for instance: distance travelled, number of contact events, total time spent in contact, mean duration of each contact event... This amount of details (number, duration, mean duration) is calculated for more than 30 behavioural events. The output file that are extracted from the raw data is a txt file, with all the variables as columns and each animal as a line.[measures_profile_cc_mice_one_mouse.txt](/uploads/299cdff63d0d1c89d1a7c6f0ce260966/measures_profile_cc_mice_one_mouse.txt)https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/4Viremia2023-05-05T11:51:33+02:00Bryan BRANCOTTEViremia# Phenotype Name
Viremia
# PhenotypeKind
Continuous
# Description
The viremia after infecting with a given virus
# Example
| Entry | Value |
|-------------------|------------------------|
| Infection Ve...# Phenotype Name
Viremia
# PhenotypeKind
Continuous
# Description
The viremia after infecting with a given virus
# Example
| Entry | Value |
|-------------------|------------------------|
| Infection Vector | Injection/mosquito/... |
| Dosage | |
| Unit | mUI/mL |
| DayAfterInfection | |
| ... | |https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/8Behavioural data examples - Experiment2023-05-05T11:51:07+02:00Elodie EYBehavioural data examples - Experiment**An experiment combines a group of mice with a specific protocol:**
For instance the experiment Exp1 tests 8 mice of 2 different strains (i.e. 16 mice) with the protocol A. The experiment Exp2 tests 32 mice of both sexes from the same ...**An experiment combines a group of mice with a specific protocol:**
For instance the experiment Exp1 tests 8 mice of 2 different strains (i.e. 16 mice) with the protocol A. The experiment Exp2 tests 32 mice of both sexes from the same strain with protocol B. This experiment table allows to gather groups of mice. It is useful for sorting of data, but maybe not necessary (just a suggestion).https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/6Behavioural data examples - Animal ID card2023-05-05T11:49:33+02:00Elodie EYBehavioural data examples - Animal ID card**Information to be available on the ID card of each animal:**
AnimalID (RFID chip number in our case)
Date of birth
Sex
Strain**Information to be available on the ID card of each animal:**
AnimalID (RFID chip number in our case)
Date of birth
Sex
Strainhttps://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/97General help/documentation2023-05-05T11:42:06+02:00Victoire BAILLETGeneral help/documentation**Generalities that need to be provided somehow to the user.**
- [x] provide a dummy infile
Write somewhere that:
- [x] input file must be tsv (or csv ? to decide)
- [x] phenotypic values must be written US/UK format: dots instead of co...**Generalities that need to be provided somehow to the user.**
- [x] provide a dummy infile
Write somewhere that:
- [x] input file must be tsv (or csv ? to decide)
- [x] phenotypic values must be written US/UK format: dots instead of comma
- [x] cc-qtl currently performs linear, not logistic regression: that means, only continuous, not binary traits can be taken into account
- [x] to satisfy the stats hypotheses underlying QTL mapping, phenotypic data must be pseudo-gaussian. It is advised that before feeding your data to ccqtl, you first plot them to see if the distribution grossly satisfies a gaussian. If it is not the case, several mathematicals transformations of your data can be considered...
- [x] what type of transformation given the data ? from R to L. Strongly right-skewed: log ; slitghly right-skewed : square-root ; left-skewed : power. See pig dingy for a generic reminder (ref = https://www.davidzeleny.net/anadat-r/doku.php/en:data_preparation)0.2.0-stableVictoire BAILLETVictoire BAILLEThttps://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/12Funnel codes des CC et RIX2023-05-05T11:25:26+02:00Xavier MONTAGUTELLIFunnel codes des CC et RIX**Schéma de croisement des CC :<br>**
Première génération :<br>
F1 x M2 -> F12 (Chr X: 1 ou 2)<br>
F3 x M4 -> M34 (Chr X : 3)<br>
F5 x M6 -> F56 (Chr X: 5 ou 6)<br>
F7 x M8 -> M78 (Chr X : 7)<br>
Deuxième génération :<br>
F12 x M34 -> F1...**Schéma de croisement des CC :<br>**
Première génération :<br>
F1 x M2 -> F12 (Chr X: 1 ou 2)<br>
F3 x M4 -> M34 (Chr X : 3)<br>
F5 x M6 -> F56 (Chr X: 5 ou 6)<br>
F7 x M8 -> M78 (Chr X : 7)<br>
Deuxième génération :<br>
F12 x M34 -> F1234 (Chr X: 1, 2 ou 4)<br>
F56 X M78 -> M5678 (Chr X : 5 ou 6)<br>
Troisième génération :<br>
F1234 x M5678 -> M et F fondateur de la CC (Chr X : 1, 2, 3, 5 ou 6)<br>
Donc lignées en position 4, 7 et 8 ne contribuent pas au Chr X de la CC.<br>
<br>
**Funnel codes :<br>**
Le funnel code (8 lettres) désigne l'ordre des 8 lignées parentales dans le croisement.<br>
ex : dans BECADHFG, B est la lignée 1, ... et G la lignée 8.<br>
<br>
**Funnel codes manquants :<br>**
Pour certaines lignées, le funnel code n'est pas connu (perte d'info lors des croisements).<br>
Le funnel code n'intervient a priori que pour le chromosome X.<br>
Générer des funnels codes aléatoires respectant la règle "478" : les fondateurs ayant contribué aux allèles portés par la lignée sur le Chr X ne doivent pas être en position 4, 7 ou 8.<br>
Tester différents codes aléatoires pour les lignées sans funnel code et voir si on obtient les mêmes matrices de genos.prob.<br>
Si c'est le cas, en choisir un une bonne fois pour toutes.<br>
<br>
**Funnel codes pour les RIX :<br>**
Les RIX sont des F1 entre 2 lignées CC. Les mâles ont hérité leur X de la lignée de la femelle. Pour les femelles, le X peut venir de l'un ou l'autre des parents.<br>
Je (XM) pense que le problème du Chr X ne concerne que les mâles et qu'il faut donc attribuer au F1 le funnel code du parent CC femelle.<br>
Pour les femelles, le Chr X se comporte plus ou moins comme un autosome, donc ça ne devrait pas poser de problème. A tester le moment venu...https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/96Definitions / help boxes2023-05-05T11:21:34+02:00Victoire BAILLETDefinitions / help boxes@rplanel here as discussed a list of "definitions"/what to put in the different "helps boxes", typically upon selection of a given file in a drop-down menu.
The idea is, for each drop-down menu, offering a default file (which will be t...@rplanel here as discussed a list of "definitions"/what to put in the different "helps boxes", typically upon selection of a given file in a drop-down menu.
The idea is, for each drop-down menu, offering a default file (which will be the first one visible in the menu), with an explanation next to it (text box, hovering a "?", UX part tbd).
Things that need to be defined as follows (tbc) ; definitions/helps will be specified as replies to this post.
- [x] Cox v38 genetic map (in "genetic map" dropdown menu)
- [x] G2F1 v38 genetic map (in "genetic map" dropdown menu)
- [x] Physical map v38 (where ? to be defined) - right now that's not an emergency bc I haven't lifted Cox to v39 nor the cc_variants sqlite ; so they'll need to stay v38 by then :sweat_smile:
- [ ] Mouse gene annotations full v38 (in "annotation" dropdown menu) (~ mouse_gene.sqlite)
- [ ] Mouse gene annotations MGI v38 (in "annotation" dropdown menu) (~ mouse_gene_MGI.sqlite)
- [ ] CC founders variants v38 (where ? to be defined) (~ cc_variants.sqlite)
Things that need to be defined, to keep for muuuch later (parce que ça sera pas bcp plus de boulot, et pour le moment on a pas encore l'ensemble des fichiers qui permettent de tout faire en v39)
- [x] Cox v39 genetic map (in "genetic map" dropdown menu) - def same as above, change version
- [x] G2F1 v39 genetic map (in "genetic map" dropdown menu) - def same as above, change version
- [x] Physical map v39 (for later)
- [ ] Mouse gene annotations full v39 (in "annotation" dropdown menu) (~ mouse_gene.sqlite)
- [ ] Mouse gene annotations MGI v39 (in "annotation" dropdown menu) (~ mouse_gene_MGI.sqlite)
- [ ] CC founders variants v39 (where ? to be defined) (~ cc_variants.sqlite)
Things that needed to have a help/information box yet do not need to be versioned and/or several options in drop-down menu:
- [x] Funnel codes (not completely true w:r to versioning though, but that would mean XM would find a way to start working on the newish CCs == bring them to IP)0.2.0-stableVictoire BAILLETVictoire BAILLEThttps://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/118checklist to ISMB abstract subm release2023-05-05T11:20:43+02:00Victoire BAILLETchecklist to ISMB abstract subm releaseThis is checklist for @vibaille and @rplanel of what needs to be done to get as of ISMB abstract submission deadline.
Work branch for that is: to-final-gitlab-orga.
On the readme/doc/test data side:
- [x] drop testdata as testdata.csv i...This is checklist for @vibaille and @rplanel of what needs to be done to get as of ISMB abstract submission deadline.
Work branch for that is: to-final-gitlab-orga.
On the readme/doc/test data side:
- [x] drop testdata as testdata.csv in testdata folder. Make it minimal, one pheno, at most two for safety, no covariates.
- [x] Readme: general intro
- [x] Readme: how to retrieve the dockers, deploy, create
- [x] Readme: getting started: description of interface, 1st encounter, what to start with
- [x] Readme: load pheno data
- [x] Readme: annotate pheno data w pheno categories and controlled vocab
- [x] Readme: plot pheno data and transform if any
- [x] Readme : QTL mapping, the difft steps: format data, calc genoprob, scan, perm, find peaks & effects, ref regions
- [x] Readme: more advanced command. Permissions, data deletion... All what is not worth telling as 101
- [x] Readme: FAQ.
- [x] for all figs in readme, hyperlink to corresponding figs to be hosted in docs/img folder
Overall/general side:
- [x] cleanup to only have relevant dirs and files in to-final-gitlab-orga. List of (very old) things to check: .gitlab/issue_templates, classes_draft.mdj, classes_draft.png, start-docker-compose.sh
- [x] ensure https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db is publicly available
- [x] once all is done, merge to-final-gitlab-orga to main so that all appears at https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db (which is path provided in abstract)
- [x] Readme: after merging to main, fix all hyperlinks in readme
- [x] License file!! (oups)
... any other thing to add ?2023-04-20https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/86Validate constant files versioning2023-05-05T11:19:00+02:00Victoire BAILLETValidate constant files versioningBefore training and anything else, need to validate and ensure versioning of all "resource" files that should ~ to Srivastava et al. (2017), namely:
- funnel codes : is latest version ? handling of crossing funnel glitches ?
- genetic m...Before training and anything else, need to validate and ensure versioning of all "resource" files that should ~ to Srivastava et al. (2017), namely:
- funnel codes : is latest version ? handling of crossing funnel glitches ?
- genetic map : keep it splitted by chromosomes ? or one for all ? Cox version ?
- physical map : keep it splitted by chr ?
- founders geno at markers
- indiv geno at markers
- markers : GigaMUGA only ?0.2.0-stableVictoire BAILLETVictoire BAILLEThttps://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/11Format des données en entrée2023-04-28T11:59:30+02:00Bryan BRANCOTTEFormat des données en entréeOn doit pouvoir prendre en entré les format LONG et WIDE
![P_20190128_124241_vHDR_Auto](/uploads/eaf371ac4d1e614e53d0273bd97bba38/P_20190128_124241_vHDR_Auto.jpg)On doit pouvoir prendre en entré les format LONG et WIDE
![P_20190128_124241_vHDR_Auto](/uploads/eaf371ac4d1e614e53d0273bd97bba38/P_20190128_124241_vHDR_Auto.jpg)https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/87Proper labelling / metadata of "Phenotypes"2023-04-28T11:57:22+02:00Victoire BAILLETProper labelling / metadata of "Phenotypes""Phenotype categories" menu in ccqtl interface, where relevant description/metadata shall be used to "qualify" informatively a phenotype. What categories to use / how to classify them"Phenotype categories" menu in ccqtl interface, where relevant description/metadata shall be used to "qualify" informatively a phenotype. What categories to use / how to classify themVictoire BAILLETVictoire BAILLEThttps://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/101Code scale-up, parallelisation, etc etc2023-04-28T11:50:22+02:00Victoire BAILLETCode scale-up, parallelisation, etc etcShort recap down there of the difft options to get cc-qtl-workflow to proceed faster:
qtl2-specific arguments:
- cores argument: add "cores = cores" in qtl2 functions that allow it, def cores as arg of Rscript ; and in the xml wrapper...Short recap down there of the difft options to get cc-qtl-workflow to proceed faster:
qtl2-specific arguments:
- cores argument: add "cores = cores" in qtl2 functions that allow it, def cores as arg of Rscript ; and in the xml wrapper Rémi takes care of VARENV that grabs defined nb of cores on galaxy instance.
- max_batch (for scan1): indicates the maximum number of phenotypes to run together; default is unlimited (hence can trigger memory pb...). Back of envelope calculation ~ upper limit to 500 pheno being analyzed at once. Phenos should apparently be considered one at a time iff LMM and not HK (https://groups.google.com/g/rqtl2-disc/c/M9clhYsM0LU for discussion)
Others:
permutation procedure ? to be thought about.https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db/-/issues/116Refactor phenotype category2023-04-19T11:17:00+02:00Remi PLANELRefactor phenotype category- upload phenotype based on column names
- Let user group them using phenotype category
## Phenotype
Il n'a **QUE** des phénotypes. ils peuvent être utilisés comme des covariables en fonction de la question. Néanmoins, certains phénot...- upload phenotype based on column names
- Let user group them using phenotype category
## Phenotype
Il n'a **QUE** des phénotypes. ils peuvent être utilisés comme des covariables en fonction de la question. Néanmoins, certains phénotypes ne sont utilisés que comme des covariables (sex, age, origine cc)
- covar fixe : données ?
- phénotypes (qui peuvent être des covar) : mesure ? phénotype quantitatif ?
## Analyse
- l'utilisateur doit préciser au moment de lancer l'analyse ce qui est covar, ce qui est phénotype
- liste des phénos (on vire les covars fixes) ?
- liste des covars (tous les phénos + les covars fixes) ?
- fournir pour les analyses un fichier séparé pour les phénotypes et pour les covarianles
-Remi PLANELRemi PLANEL